Job ID = 1295082 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,464,779 reads read : 14,464,779 reads written : 14,464,779 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:59 14464779 reads; of these: 14464779 (100.00%) were unpaired; of these: 1084042 (7.49%) aligned 0 times 10631271 (73.50%) aligned exactly 1 time 2749466 (19.01%) aligned >1 times 92.51% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2519401 / 13380737 = 0.1883 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 11:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 11:48:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:48:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 11:48:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:48:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 11:48:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:48:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:49:06: 1000000 INFO @ Mon, 03 Jun 2019 11:49:07: 1000000 INFO @ Mon, 03 Jun 2019 11:49:07: 1000000 INFO @ Mon, 03 Jun 2019 11:49:13: 2000000 INFO @ Mon, 03 Jun 2019 11:49:16: 2000000 INFO @ Mon, 03 Jun 2019 11:49:17: 2000000 INFO @ Mon, 03 Jun 2019 11:49:21: 3000000 INFO @ Mon, 03 Jun 2019 11:49:24: 3000000 INFO @ Mon, 03 Jun 2019 11:49:25: 3000000 INFO @ Mon, 03 Jun 2019 11:49:28: 4000000 INFO @ Mon, 03 Jun 2019 11:49:33: 4000000 INFO @ Mon, 03 Jun 2019 11:49:33: 4000000 INFO @ Mon, 03 Jun 2019 11:49:36: 5000000 INFO @ Mon, 03 Jun 2019 11:49:42: 5000000 INFO @ Mon, 03 Jun 2019 11:49:42: 5000000 INFO @ Mon, 03 Jun 2019 11:49:43: 6000000 INFO @ Mon, 03 Jun 2019 11:49:50: 6000000 INFO @ Mon, 03 Jun 2019 11:49:50: 6000000 INFO @ Mon, 03 Jun 2019 11:49:50: 7000000 INFO @ Mon, 03 Jun 2019 11:49:58: 8000000 INFO @ Mon, 03 Jun 2019 11:49:58: 7000000 INFO @ Mon, 03 Jun 2019 11:49:59: 7000000 INFO @ Mon, 03 Jun 2019 11:50:05: 9000000 INFO @ Mon, 03 Jun 2019 11:50:07: 8000000 INFO @ Mon, 03 Jun 2019 11:50:07: 8000000 INFO @ Mon, 03 Jun 2019 11:50:13: 10000000 INFO @ Mon, 03 Jun 2019 11:50:15: 9000000 INFO @ Mon, 03 Jun 2019 11:50:16: 9000000 INFO @ Mon, 03 Jun 2019 11:50:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:50:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:50:19: #1 total tags in treatment: 10861336 INFO @ Mon, 03 Jun 2019 11:50:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:50:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:50:20: #1 tags after filtering in treatment: 10861336 INFO @ Mon, 03 Jun 2019 11:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:50:20: #1 finished! INFO @ Mon, 03 Jun 2019 11:50:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:50:21: #2 number of paired peaks: 272 WARNING @ Mon, 03 Jun 2019 11:50:21: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Mon, 03 Jun 2019 11:50:21: start model_add_line... INFO @ Mon, 03 Jun 2019 11:50:21: start X-correlation... INFO @ Mon, 03 Jun 2019 11:50:21: end of X-cor INFO @ Mon, 03 Jun 2019 11:50:21: #2 finished! INFO @ Mon, 03 Jun 2019 11:50:21: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 11:50:21: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 11:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.10_model.r INFO @ Mon, 03 Jun 2019 11:50:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:50:23: 10000000 INFO @ Mon, 03 Jun 2019 11:50:24: 10000000 INFO @ Mon, 03 Jun 2019 11:50:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:50:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:50:30: #1 total tags in treatment: 10861336 INFO @ Mon, 03 Jun 2019 11:50:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:50:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:50:31: #1 tags after filtering in treatment: 10861336 INFO @ Mon, 03 Jun 2019 11:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:50:31: #1 finished! INFO @ Mon, 03 Jun 2019 11:50:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:50:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:50:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:50:31: #1 total tags in treatment: 10861336 INFO @ Mon, 03 Jun 2019 11:50:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:50:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:50:32: #2 number of paired peaks: 272 WARNING @ Mon, 03 Jun 2019 11:50:32: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Mon, 03 Jun 2019 11:50:32: start model_add_line... INFO @ Mon, 03 Jun 2019 11:50:32: #1 tags after filtering in treatment: 10861336 INFO @ Mon, 03 Jun 2019 11:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:50:32: #1 finished! INFO @ Mon, 03 Jun 2019 11:50:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:50:32: start X-correlation... INFO @ Mon, 03 Jun 2019 11:50:32: end of X-cor INFO @ Mon, 03 Jun 2019 11:50:32: #2 finished! INFO @ Mon, 03 Jun 2019 11:50:32: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 11:50:32: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 11:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.05_model.r INFO @ Mon, 03 Jun 2019 11:50:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:50:33: #2 number of paired peaks: 272 WARNING @ Mon, 03 Jun 2019 11:50:33: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Mon, 03 Jun 2019 11:50:33: start model_add_line... INFO @ Mon, 03 Jun 2019 11:50:33: start X-correlation... INFO @ Mon, 03 Jun 2019 11:50:33: end of X-cor INFO @ Mon, 03 Jun 2019 11:50:33: #2 finished! INFO @ Mon, 03 Jun 2019 11:50:33: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 11:50:33: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 11:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.20_model.r INFO @ Mon, 03 Jun 2019 11:50:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:50:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:51:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:51:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:51:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.10_summits.bed INFO @ Mon, 03 Jun 2019 11:51:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1836 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.20_summits.bed INFO @ Mon, 03 Jun 2019 11:51:19: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318780/SRX318780.05_summits.bed INFO @ Mon, 03 Jun 2019 11:51:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3215 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。